{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T12:26:29Z","timestamp":1775478389317,"version":"3.50.1"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T00:00:00Z","timestamp":1729468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFF1206103"],"award-info":[{"award-number":["2023YFF1206103"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFA0915500"],"award-info":[{"award-number":["2023YFA0915500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["62272449"],"award-info":[{"award-number":["62272449"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Basic Research Fund","award":["RCYX20200714114734194"],"award-info":[{"award-number":["RCYX20200714114734194"]}]},{"name":"Shenzhen Basic Research Fund","award":["KQTD20200820113106007"],"award-info":[{"award-number":["KQTD20200820113106007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Molecular docking is an invaluable computational tool with broad applications in computer-aided drug design and enzyme engineering. However, current molecular docking tools are typically implemented in languages such as C++ for calculation speed, which lack flexibility and user-friendliness for further development. Moreover, validating the effectiveness of external scoring functions for molecular docking and screening within these frameworks is challenging, and implementing more efficient sampling strategies is not straightforward.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address these limitations, we have developed an open-source molecular docking framework, OpenDock, based on Python and PyTorch. This framework supports the integration of multiple scoring functions; some can be utilized during molecular docking and pose optimization, while others can be used for post-processing scoring. In terms of sampling, the current version of this framework supports simulated annealing and Monte Carlo optimization. Additionally, it can be extended to include methods such as genetic algorithms and particle swarm optimization for sampling docking poses and protein side chain orientations. Distance constraints are also implemented to enable covalent docking, restricted docking or distance map constraints guided pose sampling. Overall, this framework serves as a valuable tool in drug design and enzyme engineering, offering significant flexibility for most protein\u2013ligand modelling tasks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>OpenDock is publicly available at: https:\/\/github.com\/guyuehuo\/opendock.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae628","type":"journal-article","created":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T17:59:19Z","timestamp":1729533559000},"source":"Crossref","is-referenced-by-count":4,"title":["OpenDock: a pytorch-based open-source framework for protein\u2013ligand docking and modelling"],"prefix":"10.1093","volume":"40","author":[{"given":"Qiuyue","family":"Hu","sequence":"first","affiliation":[{"name":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, 518000,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing, 100049,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4554-133X","authenticated-orcid":false,"given":"Zechen","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Physics, Shangdong University , Jinan, 250100,","place":["China"]}]},{"given":"Jintao","family":"Meng","sequence":"additional","affiliation":[{"name":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, 518000,","place":["China"]}]},{"given":"Weifeng","family":"Li","sequence":"additional","affiliation":[{"name":"School of Physics, Shangdong University , Jinan, 250100,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4632-4364","authenticated-orcid":false,"given":"Jingjing","family":"Guo","sequence":"additional","affiliation":[{"name":"Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Macao SAR, 999078,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2499-026X","authenticated-orcid":false,"given":"Yuguang","family":"Mu","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University , Singapore 637551,","place":["Singapore"]}]},{"given":"Sheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanghai Zelixir Biotech Co. Ltd , Shanghai, 201203,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1179-2106","authenticated-orcid":false,"given":"Liangzhen","family":"Zheng","sequence":"additional","affiliation":[{"name":"Shenzhen Zelixir Biotech Co. Ltd , Shenzhen, 518107,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4791-7540","authenticated-orcid":false,"given":"Yanjie","family":"Wei","sequence":"additional","affiliation":[{"name":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, 518000,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2024,10,21]]},"reference":[{"key":"2024111117073629900_btae628-B1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with alphafold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2024111117073629900_btae628-B2","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1093\/bib\/bbz103","article-title":"Computational\/in silico methods in drug target and lead prediction","volume":"21","author":"Agamah","year":"2020","journal-title":"Brief Bioinform"},{"key":"2024111117073629900_btae628-B3","doi-asserted-by":"crossref","first-page":"2214","DOI":"10.1093\/bioinformatics\/btv082","article-title":"Fast, accurate, and reliable molecular docking with quickvina 2","volume":"31","author":"Alhossary","year":"2015","journal-title":"Bioinformatics"},{"key":"2024111117073629900_btae628-B4","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/j.chembiol.2003.09.002","article-title":"The process of structure-based drug design","volume":"10","author":"Anderson","year":"2003","journal-title":"Chem Biol"},{"key":"2024111117073629900_btae628-B5","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1093\/bioinformatics\/btq112","article-title":"A machine learning approach to predicting protein\u2013ligand binding affinity with applications to molecular docking","volume":"26","author":"Ballester","year":"2010","journal-title":"Bioinformatics"},{"key":"2024111117073629900_btae628-B6","doi-asserted-by":"crossref","first-page":"2231","DOI":"10.1021\/acs.jcim.1c00334","article-title":"Deepbsp\u2014a machine learning method for accurate prediction of protein\u2013ligand docking structures","volume":"61","author":"Bao","year":"2021","journal-title":"J Chem Inf Model"},{"key":"2024111117073629900_btae628-B7","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1088\/0034-4885\/51\/3\/003","article-title":"The metropolis algorithm","volume":"51","author":"Bhanot","year":"1988","journal-title":"Rep Prog Phys"},{"key":"2024111117073629900_btae628-B8","volume-title":"Proceedings of COMPSTAT'2010: 19th International Conference on Computational Statistics, Paris, France, August 22\u201327, 2010, Keynote, Invited and Contributed Papers,"},{"key":"2024111117073629900_btae628-B9","author":"Corso G, Deng A, Fry B, et al. 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